The goal of the proposed research is to develop and apply theoretical simulation techniques to study the nature and energetics of protein- substrate and protein-inhibitor interactions, the mechanism of uncatalyzed solution phase reactions, and enzymatically catalyzed reactions. By increasing our understanding of existing inhibitors as well as our ability to design new inhibitors will have a major impact on improving human health. An increase in our knowledge of protein structure and function will have a major impact on biotechnology, because it will allow for the ab initio design of new proteins with increased or more selective catalytic properties. To address these issues we will subject two classes of zinc metalloenzymes to intense theoretical scrutiny. These are the human carbonic anhydrases (HCAs) and the matrix metalloproteinases (MMPs). In particular, we will look at HCAII and the MMPs stromelysin-1 (S1) and matrilysin, HCAII is of great biomedical importance because of its role in processes involving CO2, and because inhibitors are used in the treatment of glaucoma. S1 and matrilysin are important in structural modification of tissue and inhibitors are potentially useful in the treatment of arthritis. Moreover, related MMPs are involved in diseases ranging from cancer to periodontal disease. Thus, an understanding of S1 and matrilysin will shed light on related MMPs. In order to understand the structure and function of these enzymes we will develop quantum mechanical/molecular mechanical (QM/MM) methods that have improved performance, improved treatment of long-range interactions as well as the ability to determine absolute and relative binding free energies. These new methods offer capabilities beyond traditional methods and, therefore, we will obtain novel molecular-level insights regarding enzymes. These methods will be applied to the study of condensed phase reactions as well as enzyme/substrate interactions, metal ion binding, catalysis and inhibition in S1, matrilysin and HCAII. These studies will provide a molecular-level picture of the factors involved in enzyme inhibition and catalysis. We will also supply our QM/MM programs to the scientific community in order to allow others the ability to probe the structure and function of biomacromolecules using our tools.